A5089449964- Viral-associated cancers and disorders
- Cancer-related molecular mechanisms research
- Cancer Genomics and Diagnostics
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- T-cell and Retrovirus Studies
- Cytomegalovirus and herpesvirus research
- MicroRNA in disease regulation
- Prostate Cancer Treatment and Research
- Cancer, Lipids, and Metabolism
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Cancer, Hypoxia, and Metabolism
- Medical Imaging and Pathology Studies
- Mesenchymal stem cell research
- Immune Cell Function and Interaction
- RNA and protein synthesis mechanisms
- Renal and related cancers
- Epigenetics and DNA Methylation
- Genetic factors in colorectal cancer
- Lymphoma Diagnosis and Treatment
- Circular RNAs in diseases
- Renal cell carcinoma treatment
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
Tulane University
2015-2024
Cancer Genetics (United States)
2021
Louisiana Cancer Research Center
2013-2020
University of Pittsburgh
2003
Previously we described a reliable method based on immunodepletion for isolating mesenchymal stem cells (MSCs) from murine bone marrow and showed that, after intracranial transplantation, the migrated throughout forebrain cerebellum adopted neural cell fates. Here systemically administered MSCs purified by male bleomycin (BLM)-resistant BALB/c mice into female BLM-sensitive C57BL/6 recipients quantified engraftment levels in lung real-time PCR. Male DNA accounted 2.21 × 10 -5 % of total...
Abstract Mesenchymal stem cells (MSCs) are typically enriched from bone marrow via isolation of the plastic adherent, fibroblastoid cell fraction. However, adherent cultures elaborated murine an admixture and hematopoietic types. Here we report a reliable method based on immunodepletion to fractionate within cultures. The immunodepleted expressed antigens Sca‐1, CD29, CD44, CD81, CD106, marker nucleostemin (NST) but not CD11b, CD31, CD34, CD45, CD48, CD90, CD117, CD135, or transcription...
The high level of accuracy and sensitivity next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential pathogen discovery diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need stringent analysis protocols studies investigating sequence-based microbial signatures clinical samples.
Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC). Although previous investigations provide a strong link between EBV and carcinomas, these studies were performed using selected gene probes. Using cohort carcinoma RNA-seq data sets from The Cancer Genome Atlas (TCGA), we quantitative global assessment expression in assessed cellular pathway alterations. transcripts detected 17% samples but varied significantly coverage depth. In four the highest...
Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings EBV encoded microRNAs, new long non-coding RNAs as well more recent discovery over a hundred polyadenylated lytic transcripts. Here we report an additional layer identification repertoire latent and viral circular RNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, III, identified expressed from Cp promoter involving backsplicing W1 W2...
Using a simple viral genome enrichment approach, we report the de novo assembly of Akata and Mutu Epstein-Barr virus (EBV) genomes from single lane next-generation sequencing (NGS) reads. The are type I EBV strains approximately 171 kb in length. Evidence for heterogeneity was found but not strain. A comparative analysis with another four completely sequenced strains, B95-8/Raji, AG876, Mutu, GD1, demonstrated that strain is most closely related to GD1 exhibits greatest divergence II strain,...
L1 elements represent the only currently active, autonomous retrotransposon in human genome, and they make major contributions to genetic instability. The vast majority of 500 000 genome are defective, a relatively few can contribute retrotransposition process. However, there is no comprehensive approach identify specific loci that actively transcribed separate from excess L1-related sequences co-transcribed within genes. We have developed RNA-Seq procedures, as well 1200 bp 5΄ RACE product...
Annotation of herpesvirus genomes has traditionally been undertaken through the detection open reading frames and other genomic motifs, supplemented with sequencing individual cDNAs. Second generation high-density microarray studies have revealed vastly greater transcriptome complexity than is captured by existing annotation. The pervasive nature overlapping transcription throughout genomes, however, poses substantial problems in resolving transcript structures using these methods alone. We...
ABSTRACT In an attempt to explore infectious agents associated with nasopharyngeal carcinomas (NPCs), we employed our high-throughput RNA sequencing (RNA-seq) analysis pipeline, CoMPASS, investigate the presence of ectopic organisms within a number NPC cell lines commonly used by and Epstein-Barr virus (EBV) researchers. Sequencing data sets from both CNE1 HONE1 were found contain reads for human papillomavirus 18 (HPV-18). Subsequent real-time reverse transcription-PCR (RT-PCR) on panel...
Sex is an important determinant of brain microvessels (MVs) function and susceptibility to cerebrovascular neurological diseases, but underlying mechanisms are unclear. Using high throughput RNA sequencing analysis, we examined differentially expressed (DE) genes in MVs from young, male, female rats. Bioinformatics analysis the 23,786 identified indicates that 298 (1.2%) were DE using False Discovery Rate criteria (FDR; p < 0.05), which 119 (40%) 179 (60%) abundantly male MVs,...
MicroRNA miR-155 is expressed at elevated levels in human cancers including of the lung, breast, colon, and a subset lymphoid malignancies. In B cells, induced by oncogenic latency gene expression program herpesvirus Epstein-Barr virus (EBV). Two other herpesviruses, Kaposi's sarcoma-associated Marek's disease virus, encode functional homologues miR-155, suggesting role for this microRNA biology pathogenesis these viruses. Bone morphogenetic protein (BMP) signaling involved an array cellular...
Cancer develops and progresses often by inactivating p53. Here, we unveil nerve growth factor receptor (NGFR, p75NTR or CD271) as a novel p53 inactivator. activates NGFR transcription, whereas inactivates promoting its MDM2-mediated ubiquitin-dependent proteolysis directly binding to central DNA domain preventing DNA-binding activity. Inversely, ablation p53, consequently inducing apoptosis, attenuating survival, reducing clonogenic capability of cancer cells, well sensitizing human cells...
Next generation sequencing (NGS) can globally interrogate the genetic composition of biological samples in an unbiased yet sensitive manner. The objective this study was to utilize capabilities NGS investigate reported association between glioblastoma multiforme (GBM) and human cytomegalovirus (HCMV). A large-scale comprehensive virome assessment performed on publicly available datasets from Cancer Genome Atlas (TCGA), including RNA-seq primary GBM (n = 157), recurrent 13), low-grade gliomas...
Abstract We used serial analysis of gene expression to catalog the transcriptome murine mesenchymal stem cells (MSCs) enriched from bone marrow by immunodepletion. Interrogation this database, results which are delineated in appended databases, revealed that immunodepleted MSCs (IDmMSCs) highly express transcripts encoding connective tissue proteins and factors modulating T-cell proliferation, inflammation, turnover. Categorizing based on ontologies also expressed mRNAs regulate mesoderm...
ABSTRACT Using high-throughput RNA sequencing data from 50 common lymphoma cell culture models the Cancer Cell Line Encyclopedia project, we performed an unbiased global interrogation for presence of a panel 740 viruses and strains known to infect human other mammalian cells. This led findings previously identified infections by Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV), T-lymphotropic type 1 (HTLV-1). In addition, also found unreported infection one line (DEL) with...
ABSTRACT Epstein-Barr virus (EBV) reactivation involves the ordered induction of approximately 90 viral genes that participate in generation infectious virions. Using strand-specific RNA-seq to assess EBV transcriptome during reactivation, we found extensive bidirectional transcription extending across nearly entire genome. In contrast, only 4% genome is currently bidirectionally annotated. Most newly identified transcribed regions show little evidence coding potential, supporting noncoding...
We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long noncoding RNAs (vlncRNAs) are expressed during reactivation. Here we show EBV latency origin replication (oriP) is transcribed bi-directionally reactivation and both leftward (oriPtLs) rightward (oriPtRs) transcripts largely localized in nucleus. While oriPtLs most noncoding, at least some oriPtRs contain BCRF1/vIL10 open reading frame. Nonetheless, oriPtR with 5' untranslated regions may...
As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes physiologic, pathologic, pharmacologic settings. High throughput RNA sequencing specialized software to detect AS has greatly enhanced our ability determine transcriptome-wide changes. Despite the richness this data, deriving meaning from sometimes thousands events substantial bottleneck for most investigators. We present SpliceTools, suite data...
Using an enhanced RNA-Seq pipeline to analyze Epstein-Barr virus (EBV) transcriptomes, we investigated viral and cellular gene expression in the Akata cell line following B-cell-receptor-mediated reactivation. Robust induction of EBV was observed, with most genes induced >200-fold transcripts accounting for 7% all mapped reads within cell. After induction, hundreds candidate splicing events were detected using junction mapper TopHat, including a novel nonproductive event at gp350/gp220 locus...
Abstract Most hereditary tumors show aberrations in DNA repair genes or their regulators. In contrast, only a minority of sporadic alterations these genes. As result, genomic instability is currently considered an enhancer tumorigenesis rather than obligatory event this process. However, tumor heterogeneity presents significant technical challenge for most cancer genomics studies performed at less 100× mean resolution depth. To address the importance prostate carcinogenesis and progression,...
ABSTRACT Comprehensive virome analysis of RNA sequence (RNA-seq) data sets from 118 non-Hodgkin's B-cell lymphomas revealed a small subset that is positive for Epstein-Barr virus (EBV) or human herpesvirus 6B (HHV-6B), with one coinfection. EBV transcriptome expression the latency genes RPMS1, LMP1, and LMP2, sample additionally showing high level early lytic another EBNA2 expression. HHV-6B majority were transcribed.